Contacts of the helix formed by residues 16 - 47 (chain W) in PDB entry 3H1J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 16 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416N TYR* 5.0 6.7 - - + -
443N TRP* 4.8 20.2 - - - -
12W ALA 6.0 0.4 - - - -
13W LEU 3.4 2.5 - - - +
15W ARG* 1.3 89.4 - - + +
17W THR* 1.3 66.1 + - - +
18W SER* 3.0 34.0 + - - +
19W THR* 2.8 38.8 + - + +
20W PHE* 2.9 10.2 + - - +
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Residues in contact with THR 17 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416N TYR* 3.7 17.0 + - - -
442N TYR* 4.3 4.6 - - + -
443N TRP* 3.9 42.5 - - + +
3005R PEE 4.0 40.7 + - + +
15W ARG 3.3 3.4 + - - -
16W ARG* 1.3 72.7 - - - +
18W SER* 1.3 61.1 + - - +
20W PHE* 3.6 8.4 - - - +
21W ALA* 3.3 20.4 + - - +
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Residues in contact with SER 18 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W ARG* 3.2 40.9 + - - +
17W THR* 1.3 76.2 - - - +
19W THR* 1.3 73.9 + - - +
20W PHE 3.0 1.1 - - - -
21W ALA* 2.8 24.5 + - - +
22W LEU* 2.9 20.9 + - - +
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Residues in contact with THR 19 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W ALA 3.7 18.2 + - - +
13W LEU* 2.7 26.8 + - - -
16W ARG* 2.8 32.0 + - + +
18W SER* 1.3 87.5 + - - +
20W PHE* 1.3 52.0 + - - +
22W LEU* 3.8 9.0 - - - +
23W THR* 2.6 38.5 + - - -
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Residues in contact with PHE 20 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R TYR* 3.8 20.0 - - + -
40R THR* 4.0 13.9 - - + -
41R ALA* 3.7 28.9 - - + +
44R CYS* 4.3 2.9 - - - -
3005R PEE 3.7 58.6 - - + -
13W LEU 2.9 13.3 + - - +
14W PHE* 3.7 33.4 - + + +
16W ARG 2.9 13.3 + - - +
17W THR* 3.6 9.6 - - - +
19W THR* 1.3 77.7 - - - +
21W ALA* 1.3 64.1 + - - +
23W THR* 3.0 7.7 + - - -
24W VAL* 3.0 32.0 + - + +
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Residues in contact with ALA 21 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3005R PEE 3.6 33.7 - - + +
17W THR 3.3 9.5 + - - +
18W SER* 2.8 10.6 + - - +
20W PHE* 1.3 79.3 - - - +
22W LEU* 1.3 69.9 + - + +
24W VAL* 2.9 14.0 + - - +
25W VAL* 3.0 17.8 + - + +
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Residues in contact with LEU 22 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W SER* 2.9 24.1 + - - +
19W THR* 3.9 7.6 - - - +
21W ALA* 1.3 82.0 - - + +
23W THR* 1.3 57.9 + - - +
25W VAL* 3.3 11.7 + - + +
26W LEU* 2.9 32.0 + - - +
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Residues in contact with THR 23 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R ALA* 5.4 4.3 - - + -
45R VAL* 5.0 0.5 - - - +
13W LEU* 3.5 43.9 - - + +
14W PHE* 4.6 11.9 - - + -
19W THR 2.6 25.2 + - - -
20W PHE* 3.0 8.3 + - - -
22W LEU* 1.3 79.1 - - - +
24W VAL* 1.3 53.1 + - - +
26W LEU* 3.7 5.9 - - + +
27W GLY* 2.7 33.2 + - - -
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Residues in contact with VAL 24 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R ALA* 4.0 13.0 - - + +
44R CYS* 3.6 38.6 - - + +
45R VAL* 3.9 18.3 - - - +
48R ALA* 4.6 4.7 - - + -
3005R PEE 4.1 26.0 - - + -
20W PHE* 3.0 34.8 + - + +
21W ALA 2.9 8.1 + - - +
23W THR* 1.3 72.6 - - - +
25W VAL* 1.3 67.3 + - - +
28W ALA* 2.9 23.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 25 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3005R PEE 3.6 44.1 - - + +
21W ALA* 3.0 19.5 + - + +
22W LEU* 3.5 13.7 - - + +
24W VAL* 1.3 78.9 - - - +
26W LEU* 1.3 66.3 + - + +
28W ALA* 3.3 2.8 + - - +
29W VAL* 3.1 30.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W LEU 2.9 16.9 + - - +
23W THR* 3.7 7.4 - - - +
25W VAL* 1.3 77.8 - - + +
27W GLY* 1.3 66.3 + - - +
29W VAL* 3.1 10.9 - - + +
30W LEU* 3.1 46.0 + - + +
----------------------------------------------------------
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Residues in contact with GLY 27 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R VAL* 3.6 15.3 - - - -
23W THR* 2.7 22.6 + - - -
24W VAL 3.7 1.3 - - - -
26W LEU* 1.3 70.3 - - - +
28W ALA* 1.3 67.6 + - - +
30W LEU* 2.9 10.5 + - - +
31W PHE* 2.7 22.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 28 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R VAL* 3.1 23.1 - - + +
48R ALA* 4.1 17.7 - - + -
49R TYR* 4.9 3.4 - - + +
3005R PEE 3.8 26.2 - - + -
24W VAL 2.9 18.9 + - - +
25W VAL 3.6 4.5 - - - +
27W GLY* 1.3 67.7 - - - +
29W VAL* 1.3 56.6 + - - +
31W PHE* 4.1 2.6 - - - -
32W GLU* 2.5 38.0 + - - +
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Residues in contact with VAL 29 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3005R PEE 3.8 26.9 - - + +
25W VAL* 3.1 23.1 + - + +
26W LEU* 3.1 13.2 - - + +
27W GLY 3.0 0.6 + - - -
28W ALA* 1.3 78.1 - - - +
30W LEU* 1.3 68.6 + - + +
32W GLU* 3.4 3.3 + - - +
33W ARG* 3.3 37.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 30 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W LEU* 3.3 37.9 - - + +
27W GLY* 2.9 8.6 + - - +
29W VAL* 1.3 75.3 - - + +
31W PHE* 1.3 67.1 - - - +
32W GLU 3.3 0.2 + - - -
33W ARG* 3.2 34.7 + - - +
34W ALA* 3.0 24.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 31 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211Q ILE* 3.5 26.9 - - + -
214Q LEU* 4.3 20.6 - - + -
45R VAL* 3.8 20.0 - - + -
46R ALA* 4.9 6.1 - - - -
49R TYR* 3.6 39.5 - + + -
27W GLY 2.7 16.7 + - - +
28W ALA 3.4 6.5 - - - +
30W LEU* 1.3 74.7 - - - +
32W GLU* 1.3 55.5 + - - +
34W ALA* 3.5 5.0 - - + +
35W PHE* 2.7 56.7 + + + +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R TYR* 3.5 26.2 - - + -
52R LYS* 2.7 36.6 + - - +
53R ASN* 4.2 4.3 + - - -
3005R PEE 3.1 26.7 - - + +
28W ALA 2.5 21.6 + - - +
29W VAL 3.5 4.5 - - - +
31W PHE* 1.3 72.8 - - - +
33W ARG* 1.3 67.6 + - - +
36W ASP* 2.8 48.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 33 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W VAL* 3.3 19.1 + - - +
30W LEU* 3.2 46.3 + - - +
32W GLU* 1.3 81.0 - - - +
34W ALA* 1.3 65.4 + - - +
36W ASP* 3.9 3.5 - - - +
37W GLN* 3.0 43.9 + - + +
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Residues in contact with ALA 34 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W LEU 3.0 14.9 + - - +
31W PHE* 3.5 7.6 - - + +
33W ARG* 1.3 82.4 - - - +
35W PHE* 1.3 64.0 + - - +
37W GLN* 3.4 5.6 + - - +
38W GLY* 3.0 19.9 + - - -
----------------------------------------------------------
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Residues in contact with PHE 35 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207Q LYS* 3.6 37.0 - - + -
210Q LEU* 3.7 31.2 - - + -
211Q ILE* 3.5 30.1 - - + -
49R TYR* 3.3 30.7 - + - -
31W PHE* 2.7 48.7 + + + +
32W GLU* 3.7 2.2 - - - +
34W ALA* 1.3 74.6 - - - +
36W ASP* 1.3 56.9 + - - +
38W GLY* 3.2 0.6 + - - -
39W ALA* 2.7 38.2 + - + +
----------------------------------------------------------
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Residues in contact with ASP 36 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207Q LYS* 3.1 18.9 + - - +
49R TYR* 2.5 25.7 + - - -
53R ASN* 5.1 1.7 + - - +
3009R PLC 3.7 4.7 + - - -
32W GLU* 2.8 48.9 + - - +
33W ARG* 3.9 3.7 - - - +
35W PHE* 1.3 75.0 - - - +
37W GLN* 1.3 61.6 + - + +
39W ALA* 3.7 3.1 - - - +
40W ASP* 2.6 37.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 37 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ARG* 3.0 35.9 + - + +
34W ALA* 3.8 5.2 - - - +
36W ASP* 1.3 78.2 - - + +
38W GLY* 1.3 65.3 + - - +
40W ASP* 3.1 6.3 + - - +
41W ALA* 2.8 23.4 + - - +
----------------------------------------------------------
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Residues in contact with GLY 38 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W ALA 3.0 11.7 + - - -
35W PHE 3.7 2.2 - - - -
37W GLN* 1.3 79.8 - - - +
39W ALA* 1.3 55.8 + - - +
41W ALA* 3.2 9.3 + - - +
42W ILE* 2.9 38.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 39 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203Q ARG* 5.7 0.9 - - - -
206Q LEU* 3.8 10.1 - - + +
207Q LYS* 3.7 38.4 - - + -
210Q LEU* 5.2 5.6 - - + -
35W PHE* 2.7 31.3 + - + +
36W ASP 3.7 0.9 - - - +
38W GLY* 1.3 70.7 - - - +
40W ASP* 1.3 58.7 + - - +
42W ILE* 3.1 12.7 + - - +
43W PHE* 2.9 27.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP 40 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203Q ARG* 3.1 39.9 + - - +
207Q LYS* 3.9 15.6 + - - -
3009R PLC 4.8 9.4 - - - +
36W ASP* 2.6 24.0 + - - +
37W GLN* 3.5 5.4 - - - +
39W ALA* 1.3 75.2 - - - +
41W ALA* 1.3 57.8 + - - +
43W PHE* 2.9 3.2 + - - -
44W GLU* 2.7 47.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 41 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W GLN 2.8 13.6 + - - +
38W GLY* 3.2 14.6 - - - +
40W ASP* 1.3 75.8 - - - +
42W ILE* 1.3 58.7 + - + +
44W GLU* 3.8 6.0 - - - +
45W HIS* 2.9 33.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 42 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206Q LEU* 4.2 14.1 - - + -
210Q LEU* 4.8 15.3 - - + -
38W GLY 2.9 26.4 + - - +
39W ALA* 3.4 9.9 - - - +
41W ALA* 1.3 73.8 - - + +
43W PHE* 1.3 60.9 + - - +
45W HIS* 3.8 5.1 + - - +
46W LEU* 3.0 50.0 + - + +
----------------------------------------------------------
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Residues in contact with PHE 43 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q LEU* 3.3 32.3 - - + -
20Q ALA* 4.1 18.2 - - + -
199Q ASP* 3.7 21.5 - - + -
202Q LYS* 4.1 7.9 - - + -
203Q ARG* 3.2 70.7 - - + +
206Q LEU* 4.1 14.6 - - + +
39W ALA 2.9 13.6 + - - +
40W ASP 3.4 6.5 - - - +
42W ILE* 1.3 73.3 - - - +
44W GLU* 1.3 67.9 + - - +
46W LEU* 3.1 14.6 + - + +
47W ASN* 3.2 33.2 + - - -
51W LEU* 4.8 6.3 - - + -
----------------------------------------------------------
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Residues in contact with GLU 44 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203Q ARG* 3.6 22.1 + - - +
40W ASP* 2.7 32.9 + - - +
41W ALA* 3.9 4.9 - - - +
43W PHE* 1.3 72.9 - - - +
45W HIS* 1.3 60.1 + - - +
47W ASN 3.2 18.6 + - - +
48W GLU* 3.3 11.8 + - - +
51W LEU* 4.2 20.6 - - + -
53W LYS* 3.0 47.6 + - - +
54W HIS* 3.8 10.3 + - - +
----------------------------------------------------------
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Residues in contact with HIS 45 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W ALA 2.9 18.6 + - - +
42W ILE* 3.8 6.3 - - - +
44W GLU* 1.3 76.1 - - - +
46W LEU* 1.3 74.8 + - + +
47W ASN 2.9 10.6 + - - -
48W GLU* 3.3 28.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q LEU* 3.6 39.7 - - + +
19Q SER* 5.7 0.7 - - - -
206Q LEU* 5.2 0.4 - - + -
42W ILE* 3.0 37.9 + - + +
43W PHE* 3.1 9.7 + - + +
45W HIS* 1.3 89.6 - - + +
47W ASN* 1.3 66.2 + - - +
48W GLU 3.8 0.9 - - - -
50W LYS* 5.2 2.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 47 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q LEU 2.7 26.4 + - - -
19Q SER* 3.5 3.0 - - - -
20Q ALA* 2.6 37.1 + - + +
43W PHE* 3.2 33.3 + - + +
44W GLU 3.3 4.7 - - - +
45W HIS 2.9 2.2 + - - -
46W LEU* 1.3 84.5 - - - +
48W GLU* 1.3 64.4 + - - +
50W LYS* 3.1 37.8 + - + +
51W LEU* 3.8 11.4 - - + +
54W HIS* 3.2 12.0 + - - -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il